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Sample GSM5174750 Query DataSets for GSM5174750
Status Public on Jun 03, 2021
Title prostate_cancer_primary_260
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 3
secondary gleason: 4
decipher risk group: Average
race: African American
Extracted molecule total RNA
Extraction protocol After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.
Label biotin
Label protocol RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials and protocols
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G
Description PCA.260
Data processing Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps
 
Submission date Mar 16, 2021
Last update date Jun 03, 2021
Contact name Elai Davicioni
E-mail(s) elai.davicioni@veracyte.com
Organization name Veracyte, Inc
Street address 9725 Lusk Blvd
City San Diego
State/province California
ZIP/Postal code 92121
Country USA
 
Platform ID GPL5175
Series (1)
GSE169038 Comparative Analysis of 1,152 African-American and European-American Men with Prostate Cancer Identifies Distinct Genomic and Immunological Differences

Data table header descriptions
ID_REF
VALUE SCAN normalized signal estimates

Data table
ID_REF VALUE
2315554 0.401802403142857
2315633 -0.0348178665384615
2315674 -0.0778106905263158
2315739 -0.06445287
2315894 -0.40491154125
2315918 1.1378271575
2315951 -0.363737643529412
2316218 0.8140855975
2316245 0.0115223194
2316379 0.314033947301587
2316558 0.6836380628125
2316605 -0.219182585529412
2316746 0.247704090416667
2316905 -0.36115111625
2316953 -0.0270853671962617
2317246 0.053321233255814
2317317 -0.215799175438597
2317434 0.2252753634375
2317472 0.0051298825
2317512 -0.0187070083333333

Total number of rows: 22011

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM5174750_260.CEL.gz 20.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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